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{
"code": "SASDVG6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).",
"publication": {
"title": "Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).",
"author_list": "Ahmed FH, Liu JW, Royan S, Warden AC, Esquirol L, Pandey G, Newman J, Scott C, Peat TS",
"journal": "Commun Biol",
"doi": "10.1038/s42003-024-07336-6",
"pmid": "39702827",
"published_date": "2024 Dec 19"
},
"status": "released",
"submitted_date": "2024-08-26",
"released_date": "2024-12-23"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVG6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVG6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVG6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVG6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVG6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 2M",
"resolution": 172.0
},
"name": "Australian Synchrotron",
"city": "Melbourne",
"country": "Australia",
"beamline_name": "BioSAXS",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "2-nitroimidazole nitrohydrolase (T2I, G14D, K73R)",
"short_name": "NnhA",
"sequence": "MHHHHHHMITVDKRPSSRGYDDWRLSDIPQYKDGISTYEFVRATHEADYRTHQAEPVAGRTFGFNGIGRLTEVALHMPTRYTLHDQSSQYKESPSFFQGLMGVPDRGPVDLAAFQRETEELATAFENNGIKVHWVDYPEEPANPYGPLMGHVFLSWGSIWRGGSVISRFGFLPGMVGVSEYLAKWAWNTLNIPPLVAITEGAMEPGACNMIADEVLVTCLSASYDQRGTDQLVAAISKTSGTEEFHNLQLRPAVEGFFNKATGACAhPdININAIDVGKLVVSPAALDWDARTWLYDNNFELIEADPDEQREFLAPCnVLLLEPGKVIAHADCHKTNQKIRDAGVEVIEVTGTEIRKAcGGIKcRVMQINREPGPTLADVRNRVWR",
"organism": "Mycobacterium sp. (strain JS330)",
"uniprot_code": "F4ZCI3",
"uniprot_range_first": 1,
"uniprot_range_last": 379,
"oligomerization": "hexamer",
"molecular_type": "protein",
"uniprot_sequence": "MTTVDKRPSSRGYGDWRLSDIPQYKDGISTYEFVRATHEADYRTHQAEPVAGRTFGFNGI\nGRLTEVALHMPTKYTLHDQSSQYKESPSFFQGLMGVPDRGPVDLAAFQRETEELATAFEN\nNGIKVHWVDYPEEPANPYGPLMGHVFLSWGSIWRGGSVISRFGFLPGMVGVSEYLAKWAW\nNTLNIPPLVAITEGAMEPGACNMIADEVLVTCLSASYDQRGTDQLVAAISKTSGTEEFHN\nLQLRPAVEGFFNKATGACAHPDININAIDVGKLVVSPAALDWDARTWLYDNNFELIEADP\nDEQREFLAPCNVLLLEPGKVIAHADCHKTNQKIRDAGVEVIEVTGTEIRKACGGIKCRVM\nQINREPGPTLADVRNRVWR",
"mw": 43.08,
"total_mw": 258.48,
"number_molecules": 6,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Soluble NnhA from Mycobacterium sp. JS330 (carrying the point mutations T2I, G14D K73R). The protein construct used for SAXS contains an additional non-native N-terminal polyhistidine tag (MHHHHHH)."
}
],
"buffer": {
"name": "25 mM Tris-HCl, 150 mM NaCl, 5% (v/v) glycerol",
"concentration_unit": null,
"comment": "TBS+G",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.6,
"deuteration": null
},
"purity_method": null,
"name": "2-nitroimidazole nitrohydrolase",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Aarhus, Denmark",
"full_name": "Aarhus University",
"webpage": "http://www.au.dk"
}
],
"contributor_name": "Santana",
"contributor_surname": "Royan",
"orcid": "https://orcid.org/0000-0002-2312-3463"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-08-06",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 1.0,
"number_of_frames": 29,
"wavelength": 0.1,
"sample_detector_distance": 3.151,
"concentration_min": null,
"concentration_max": 3.5,
"sample_volume": 50.0,
"flow_rate": 0.4,
"s_min": 0.068,
"s_max": 3.998,
"total_exposure_time": null,
"seccolumn": 29
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVG6_fit1_model1_img.png",
"software": "REFMAC",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVG6_fit1_model1.pdb",
"model_mw": 246.5,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1112
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVG6_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.404,
"p_value": 0.0,
"fit_residual_plot": "SASDVG6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVG6_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVG6_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVG6_fit2_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/refine_A_S_ZB_Nnh035_S200_e3cb87d9_E1.log",
"symmetry": null,
"comment": null,
"user": 1112
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVG6_fit2_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.62,
"p_value": 0.5596,
"fit_residual_plot": "SASDVG6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVG6_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_A_S_ZB_Nnh035_S200_e3cb87d9_E1_VBIdNNK.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The molecular weight estimate (243 kDa) was calculated from Bayesian Inference (84.5% probability) in the molecular weight range credibility interval spanning 221.1 kDa to 372.7 kDa (98.7% probability).",
"experiment_description": "Synchrotron SAXS data from solutions of 2-nitroimidazole nitrohydrolase in 25 mM Tris-HCl, 150 mM NaCl, 5% (v/v) glycerol, pH 7.6 were collected on the BioSAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 2M detector at a sample-detector distance of 3.2 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 3.5 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 200 5/150 column at 25°C. 29 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 242.6,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.01162,
"pddf_i0_error": 1.64e-05,
"guinier_i0": 0.011686,
"guinier_i0_error": null,
"pddf_rg": 4.49,
"pddf_rg_error": 0.05,
"guinier_rg": 4.558,
"guinier_rg_error": 0.256,
"pddf_dmax": 12.6,
"pddf_dmax_error": 0.1,
"porod_volume": 363.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 47,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVG6_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-12-23T09:54:52.986675+01:00",
"bragg_peak": []
}
